another experiment
Evangeline Reynolds
2026-01-29
gganatogram’s data experiment
https://github.com/jespermaag/gganatogram
The data isn’t stored w/ sf format which the ggregions process requires.. Can’t seem to figure how it works in the original api, but not well when translated…
library(tidyverse)
library(gganatogram)
gganatogram::mmFemale_list |>
bind_rows() |>
remove_missing() |>
ggplot() +
aes(x, -y, group = group, color = id) +
geom_polygon(show.legend = F) +
coord_equal()
to_sf_routine <- function(data){
data |>
mutate(y = -y) |>
sf::st_as_sf(coords = c("x", "y"), agr = "constant") |>
group_by(id, group) |>
summarize(do_union = F) |>
ungroup() |>
group_by(id, group) |>
summarise() |>
mutate(geometry = geometry |> sf::st_cast("POLYGON")) |>
mutate(geometry = geometry |> sf::st_cast("MULTIPOLYGON")) |>
ungroup()
}
mm_female_sf <- gganatogram::mmFemale_list |>
bind_rows() |>
# filter(x != 0, y != 0, y < -2) |>
remove_missing() |>
to_sf_routine() |>
rename(organ = id)
mm_female_sf |>
ggplot() +
geom_sf(aes(geometry = geometry)) +
coord_sf()
# compare
ggseg::aseg$data$geometry## Geometry set for 29 features
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -0.5 ymin: 0 xmax: 7.061358 ymax: 3.203063
## CRS: NA
## First 5 geometries:geom_organ <- ggregions::write_geom_region_locale(mm_female_sf)
stamp_organ <- ggregions::write_stamp_region_locale(mm_female_sf)
mm_female_sf$organ |> sample(20)## [1] "peripheral_nervous_system" "peripheral_nervous_system"
## [3] "peripheral_nervous_system" "peripheral_nervous_system"
## [5] "adrenal_gland" "lymph_node"
## [7] "UBERON_0000947" "femur"
## [9] "peripheral_nervous_system" "UBERON_0000947"
## [11] "peripheral_nervous_system" "reproductive_system"
## [13] "UBERON_0000947" "peripheral_nervous_system"
## [15] "peripheral_nervous_system" "peripheral_nervous_system"
## [17] "UBERON_0000947" "peripheral_nervous_system"
## [19] "peripheral_nervous_system" "peripheral_nervous_system"ggplot() +
stamp_organ() +
stamp_organ(keep = "aorta", fill = "darkred") +
stamp_organ(keep = "brain", fill = "darkseagreen") +
stamp_organ(keep = "blood_vessel", fill = "orange")
original mouse gganatogram api
It looks great, but maybe the hard-ish thing is navigating it?
# original api
gganatogram(data = mmFemale_key,
outline = T,
fillOutline='#440154FF',
organism = 'mouse',
sex='female',
fill="value") +
theme_void() +
scale_fill_viridis_c() +
coord_equal()
cell_sf <- gganatogram::cell_list[[1]] |>
bind_rows() |>
# filter(x != 0, y != 0, y < -2) |>
remove_missing() |>
to_sf_routine() |>
rename(organelle = id)
cell_sf |>
ggplot() +
geom_sf(aes(geometry = geometry), alpha = .2) +
coord_sf()
geom_organelle <- ggregions::write_geom_region_locale(cell_sf)
stamp_organelle <- ggregions::write_stamp_region_locale(cell_sf)
cell_sf## Simple feature collection with 1088 features and 2 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: 5.4 ymin: -483.4 xmax: 606.7 ymax: -8.4
## CRS: NA
## # A tibble: 1,088 × 3
## organelle group geometry
## <chr> <chr> <MULTIPOLYGON>
## 1 actin_filaments 6_10 (((43.4 -268.8, 52.5 -250.1, 62.4 -231.9, 74.4 -214.6,…
## 2 actin_filaments 6_11 (((111 -398.1, 113.7 -400.7, 116.4 -403.2, 96.6 -396.2…
## 3 actin_filaments 6_12 (((112.1 -396.9, 112.6 -397.1, 113.2 -397.3, 121 -400.…
## 4 actin_filaments 6_13 (((170.7 -422.4, 175.3 -423.8, 179.9 -425.2, 184.8 -42…
## 5 actin_filaments 6_14 (((197.2 -430.3, 203.4 -432.1, 209.7 -433.9, 206.5 -43…
## 6 actin_filaments 6_15 (((554.9 -230.1, 554.3 -238.9, 553.9 -247.6, 537.5 -17…
## 7 actin_filaments 6_16 (((554.6 -192.2, 556.1 -196.3, 557.6 -200.4, 557.1 -20…
## 8 actin_filaments 6_17 (((557.9 -245.2, 559.4 -261.7, 560.9 -278.7, 559 -269.…
## 9 actin_filaments 6_18 (((523 -91.4, 531 -97, 537.9 -102.8, 543.2 -128.5, 547…
## 10 actin_filaments 6_19 (((512.7 -82.2, 512 -80.5, 511.3 -78.8, 519.4 -82.2, 5…
## # ℹ 1,078 more rowsggplot() +
stamp_organelle(alpha = .2) +
stamp_organelle(keep = "actin_filaments", fill = "orange", alpha = .1) +
stamp_organelle(keep = "endoplasmic_reticulum", fill = "darkred") 
Trying human anatomy with same routing
length(gganatogram::hgFemale_list)## [1] 204# fix so that all data frames can be combined with bind_rows
# the groups are numeric and character so using bind_rows fails
female_sf <- gganatogram::hgFemale_list[c(1:156, 180:195)] |> # return to this!!
bind_rows() |>
remove_missing() |>
to_sf_routine()
stamp_organ <- ggregions::write_stamp_region_locale(female_sf)
ggplot() +
stamp_organ(alpha = .2) +
stamp_organ(keep = "lung",
fill = "plum3") +
stamp_organ(keep = "stomach",
fill = "cornsilk") +
stamp_organ(keep = "heart",
fill = "coral") +
stamp_organ(keep = "brain",
fill = "pink3")
male_sf <- gganatogram::hgMale_list[2:155] |>
bind_rows() |>
# filter(x != 0, y != 0, y < -2) |>
remove_missing() |>
to_sf_routine()
ggplot(female_sf) +
aes(geometry = geometry) +
geom_sf(alpha = .2)
ggplot(male_sf) +
aes(geometry = geometry) +
geom_sf(alpha = .2)
teethr’s data experiment
https://github.com/bbartholdy/teethr
library(tidyverse)
library(teethr)
teeth_ref_data <- dental_arcade_mapping |>
as_tibble() |>
left_join(tooth_notation |>
select(tooth = text, fdi = FDI, standard = standards)
)head(teeth_ref_data) # are there other ids? like just number of tooth?## # A tibble: 6 × 4
## tooth geometry fdi standard
## <chr> <POLYGON> <chr> <chr>
## 1 URM2 ((65.18537 293.3849, 65.71057 295.1088, 66.38935 296.496… 17 2
## 2 URM1 ((74.4591 325.7847, 75.55431 326.5688, 76.88258 327.0586… 16 3
## 3 URP2 ((76.59484 342.573, 77.43558 343.7596, 78.59217 344.6295… 15 4
## 4 URP1 ((86.86233 359.6018, 86.86725 360.529, 87.02025 360.8659… 14 5
## 5 URC1 ((101.1985 370.3966, 101.3456 371.2152, 101.6861 371.999… 13 6
## 6 URI2 ((123.4955 387.3634, 123.4955 387.3634, 124.5163 387.779… 12 7library(ggregions)
geom_tooth <- ggregions::write_geom_region_locale(teeth_ref_data)
geom_tooth_text <- write_geom_region_text_locale(teeth_ref_data)
stamp_tooth <- write_stamp_region_locale(teeth_ref_data)
stamp_tooth_text <- write_stamp_region_text_locale(teeth_ref_data)
ggplot() +
stamp_tooth()
last_plot() +
stamp_tooth_text(size = 2)
ggplot() +
stamp_tooth() +
stamp_tooth_text(size = 2,
aes(label = after_stat(fdi)))
ggplot() +
stamp_tooth() +
stamp_tooth_text(size = 2,
aes(label = after_stat(standard)))
caries_ratios <- mb11_caries %>%
dental_longer(-id) %>%
dental_join() %>%
count_caries(caries = score, no_lesion = "none") %>% # convert location to lesion count
group_by(tooth) %>%
dental_ratio(count = caries_count) %>%
dental_recode(tooth, "FDI", "text")
head(caries_ratios)## # A tibble: 6 × 4
## tooth n count ratio
## <chr> <int> <dbl> <dbl>
## 1 URI1 35 4 0.114
## 2 URI2 31 4 0.129
## 3 URC1 35 7 0.2
## 4 URP1 34 3 0.0882
## 5 URP2 23 5 0.217
## 6 URM1 32 7 0.219caries_ratios |>
ggplot() +
stamp_tooth() +
aes(tooth = tooth,
fill = ratio) +
geom_tooth()
last_plot() +
geom_tooth(keep = c("LLM1", "URM3")) |>
ggfx::with_outer_glow("red") +
geom_tooth_text(keep = c("LLM1", "URM3"),
label = "😬",
hjust = -0.5) 
aseg X data
library(ggseg)
coronal_ref_data <- ggseg::aseg$data |>
filter(side == "coronal") |> # just look at coronal for the nuttiness.
group_by(region) |>
summarise(geometry = sf::st_combine(geometry)) |>
select(region = region, everything())
coronal_ref_data |> pull(region)## [1] "amygdala" "caudate" "hippocampus"
## [4] "lateral ventricle" "pallidum" "putamen"
## [7] "thalamus proper" "ventral DC" NAlibrary(ggregions)
geom_region <- write_geom_region_locale(ref_data = coronal_ref_data)
stamp_region <- write_stamp_region_locale(ref_data = coronal_ref_data)
geom_region_text <- write_geom_region_text_locale(ref_data = coronal_ref_data)
stamp_region_text <- write_stamp_region_text_locale(ref_data = coronal_ref_data)
ggplot() +
stamp_region() +
stamp_region(keep = "hippocampus", fill = "blue")
ggplot() +
stamp_region() +
stamp_region_text(check_overlap = T)
tribble(~activity, ~segment,
.2, "hippocampus",
.5, "amygdala",
.7, "thalamus proper") |>
ggplot() +
stamp_region() +
aes(region = segment,
fill = activity) +
geom_region() 